Charitywatch.org, put of the American Institute of Philanthropy, grades charities for how well they use the funds towards their stated missions. The higher percentage of their income they use towards the mission determines their grade.

Scroll down on this page (http://www.charitywatch.org/toprated.html) to "Veterans and Military" and this is what you'll see:
VETERANS & MILITARY/GRADE
Armed Services YMCA of the USA/A–
Fisher House Foundation/A+
Homes For Our Troops/A
Intrepid Fallen Heroes Fund/A+
Iraq & Afghanistan Veterans of America/A
National Military Family Association/A
Operation Homefront – N.O./A
Semper Fi Fund / Injured Marine Semper Fi Fund/A+

For the record, there has been a lot of controversy over the "Wounded Warrior" Fund because there are several organizations misrepresenting themselves as original/true/legitimate org and it's very easy to donate to one of the fakes. Several even use the original groups logo illegally.